548 related articles for article (PubMed ID: 19305407)
1. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting.
Hesselberth JR; Chen X; Zhang Z; Sabo PJ; Sandstrom R; Reynolds AP; Thurman RE; Neph S; Kuehn MS; Noble WS; Fields S; Stamatoyannopoulos JA
Nat Methods; 2009 Apr; 6(4):283-9. PubMed ID: 19305407
[TBL] [Abstract][Full Text] [Related]
2. Footprints by deep sequencing.
Hager G
Nat Methods; 2009 Apr; 6(4):254-5. PubMed ID: 19333240
[No Abstract] [Full Text] [Related]
3. High-resolution mapping of in vivo genomic transcription factor binding sites using in situ DNase I footprinting and ChIP-seq.
Chumsakul O; Nakamura K; Kurata T; Sakamoto T; Hobman JL; Ogasawara N; Oshima T; Ishikawa S
DNA Res; 2013 Aug; 20(4):325-38. PubMed ID: 23580539
[TBL] [Abstract][Full Text] [Related]
4. Genomic footprinting.
Vierstra J; Stamatoyannopoulos JA
Nat Methods; 2016 Mar; 13(3):213-21. PubMed ID: 26914205
[TBL] [Abstract][Full Text] [Related]
5. Survey of protein-DNA interactions in Aspergillus oryzae on a genomic scale.
Wang C; Lv Y; Wang B; Yin C; Lin Y; Pan L
Nucleic Acids Res; 2015 May; 43(9):4429-46. PubMed ID: 25883143
[TBL] [Abstract][Full Text] [Related]
6. Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection.
Yardımcı GG; Frank CL; Crawford GE; Ohler U
Nucleic Acids Res; 2014 Oct; 42(19):11865-78. PubMed ID: 25294828
[TBL] [Abstract][Full Text] [Related]
7. Molecular Co-occupancy Identifies Transcription Factor Binding Cooperativity In Vivo.
Sönmezer C; Kleinendorst R; Imanci D; Barzaghi G; Villacorta L; Schübeler D; Benes V; Molina N; Krebs AR
Mol Cell; 2021 Jan; 81(2):255-267.e6. PubMed ID: 33290745
[TBL] [Abstract][Full Text] [Related]
8. Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data.
Piper J; Elze MC; Cauchy P; Cockerill PN; Bonifer C; Ott S
Nucleic Acids Res; 2013 Nov; 41(21):e201. PubMed ID: 24071585
[TBL] [Abstract][Full Text] [Related]
9. An expansive human regulatory lexicon encoded in transcription factor footprints.
Neph S; Vierstra J; Stergachis AB; Reynolds AP; Haugen E; Vernot B; Thurman RE; John S; Sandstrom R; Johnson AK; Maurano MT; Humbert R; Rynes E; Wang H; Vong S; Lee K; Bates D; Diegel M; Roach V; Dunn D; Neri J; Schafer A; Hansen RS; Kutyavin T; Giste E; Weaver M; Canfield T; Sabo P; Zhang M; Balasundaram G; Byron R; MacCoss MJ; Akey JM; Bender MA; Groudine M; Kaul R; Stamatoyannopoulos JA
Nature; 2012 Sep; 489(7414):83-90. PubMed ID: 22955618
[TBL] [Abstract][Full Text] [Related]
10. A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data.
Chen X; Hoffman MM; Bilmes JA; Hesselberth JR; Noble WS
Bioinformatics; 2010 Jun; 26(12):i334-42. PubMed ID: 20529925
[TBL] [Abstract][Full Text] [Related]
11. Analysis of computational footprinting methods for DNase sequencing experiments.
Gusmao EG; Allhoff M; Zenke M; Costa IG
Nat Methods; 2016 Apr; 13(4):303-9. PubMed ID: 26901649
[TBL] [Abstract][Full Text] [Related]
12. Global reference mapping of human transcription factor footprints.
Vierstra J; Lazar J; Sandstrom R; Halow J; Lee K; Bates D; Diegel M; Dunn D; Neri F; Haugen E; Rynes E; Reynolds A; Nelson J; Johnson A; Frerker M; Buckley M; Kaul R; Meuleman W; Stamatoyannopoulos JA
Nature; 2020 Jul; 583(7818):729-736. PubMed ID: 32728250
[TBL] [Abstract][Full Text] [Related]
13. Genomic Footprinting Analyses from DNase-seq Data to Construct Gene Regulatory Networks.
Moyano TC; Gutiérrez RA; Alvarez JM
Methods Mol Biol; 2021; 2328():25-46. PubMed ID: 34251618
[TBL] [Abstract][Full Text] [Related]
14. ChIP-nexus enables improved detection of in vivo transcription factor binding footprints.
He Q; Johnston J; Zeitlinger J
Nat Biotechnol; 2015 Apr; 33(4):395-401. PubMed ID: 25751057
[TBL] [Abstract][Full Text] [Related]
15. XL-DNase-seq: improved footprinting of dynamic transcription factors.
Oh KS; Ha J; Baek S; Sung MH
Epigenetics Chromatin; 2019 Jun; 12(1):30. PubMed ID: 31164146
[TBL] [Abstract][Full Text] [Related]
16. BinDNase: a discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data.
Kähärä J; Lähdesmäki H
Bioinformatics; 2015 Sep; 31(17):2852-9. PubMed ID: 25957350
[TBL] [Abstract][Full Text] [Related]
17. Molecular and structural considerations of TF-DNA binding for the generation of biologically meaningful and accurate phylogenetic footprinting analysis: the LysR-type transcriptional regulator family as a study model.
Oliver P; Peralta-Gil M; Tabche ML; Merino E
BMC Genomics; 2016 Aug; 17(1):686. PubMed ID: 27567672
[TBL] [Abstract][Full Text] [Related]
18. Genome-wide footprinting: ready for prime time?
Sung MH; Baek S; Hager GL
Nat Methods; 2016 Mar; 13(3):222-228. PubMed ID: 26914206
[TBL] [Abstract][Full Text] [Related]
19. High-resolution footprinting of sequence-specific protein-DNA contacts.
Storek MJ; Ernst A; Verdine GL
Nat Biotechnol; 2002 Feb; 20(2):183-6. PubMed ID: 11821865
[TBL] [Abstract][Full Text] [Related]
20. DNase footprint signatures are dictated by factor dynamics and DNA sequence.
Sung MH; Guertin MJ; Baek S; Hager GL
Mol Cell; 2014 Oct; 56(2):275-285. PubMed ID: 25242143
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
